To investigate the germplasm resources and genetic diversity of the wild population Parapenaeopsis hardwickii, 558 base of the 16S rRNA and 688 bp base of the COⅠ gene sequences were obtained from P. hardwickii wild populations by PCR amplification. T, C, A and G base content of 16S rRNA gene sequences were 35.76%, 19.48%, 26.74% and 17.88%, while COⅠ gene sequences were 35.36%, 12.68%, 30.54% and 21.43% respectively. One haplotype and no polymorphic sites were detected in 16S rRNA gene sequences, while 7 haplotypes and 6 polymorphic sites were in COⅠ gene sequences, including 5 singleton variable sites and 1 parsimony informative sites. The variations of COⅠ gene sequences were more than 16S rRNA gene sequences, showing that COⅠ gene sequences were adaptive for genetic diversity analysis in P. hardwickii. The molecular phylogentic analysis based on 16S rRNA and COⅠ gene sequences were not consistent with each other, indicating that P. hardwickii was a sole branch in the genus Parapenaeopsis, and had closer relationships with Parapenaeopsis tenella and Parapenaeopsis hungerfordi. Based on the genetic distance of COⅠ gene sequences, the differentiation time of 12 shrimp species were deduced, and the results showed that the radiation differentiation time of genus Parapenaeopsis was between the Late Miocene Epoch and the Early Pliocene Epoch.